The report presents the methodologies that JRC/SETIS applies for the evaluation of selected key performance indicators measuring progress in research and innovation in Europe, and provides the necessary theoretical background to underpin the SETIS contributions to the State of the Energy Union reports. It addresses key conceptual and operational points that are important for the interpretation and use of these results in the policy debate, such as the timing of data availability, information sources, methodological caveats, or the level of disaggregation of reported results.